HPC maintenance scheduled for January 7 – 9

By | Flux, General Interest, News | No Comments

To accommodate upgrades to software and operating systems, Flux, Armis, and their storage systems (/home and /scratch) will be unavailable starting at 9am Saturday, January 7th, returning to service on Monday, January 9th.  Additionally, external Turbo mounts will be unavailable 11pm Saturday, January 7th, until 7am Sunday, January 8th.

During this time, the following updates are planned:

  • Operating system and software updates (minor updates) on Flux and Armis.  This should not require any changes to user software or processes.
  • Resource manager and job scheduling software updates.
  • Operating system updates on Turbo.

For HPC jobs, you can use the command “maxwalltime” to discover the amount of time before the beginning of the maintenance. Jobs that cannot complete prior to the beginning of the maintenance will be able to start when the clusters are returned to service.

We will post status updates on our Twitter feed ( https://twitter.com/arcts_um ) and send an email to all HPC users when the outage has been completed.

U-M team uses Flux HPC cluster for pre-surgery simulations

By | Flux, General Interest, News | No Comments

Last summer, Alberto Figueroa’s BME lab at the University of Michigan achieved an important “first” – using computer-generated blood flow simulations to plan a complex cardiovascular procedure.

“I believe this is the first time that virtual surgical planning was done for real and not as a retrospective theoretical exercise ,” says Figueroa.

Using a patient’s medical and imaging data, Figueroa was able to create a model of her unique vasculature and blood flow, then use it to guide U-M pediatric cardiologists Aimee Armstrong, Martin Bocks, and Adam Dorfman in placing a graft in her inferior vena cava to help alleviate complications from pulmonary arteriovenous malformations (PAVMs). The simulations were done using the Flux HPC cluster.

Read more…

Cluster upgrades completed

By | Flux, General Interest, News | No Comments

Several key systems were updated and improved during the ARC-TS HPC summer maintenance from July 16 – 23, 2016.

Among other improvements, the updates provide access to more current versions of popular software and libraries, allow new features and more consistent runtimes for job scheduling, and migrate two-factor authentication for the login servers to a new system.

The improvements included:

  • Upgrades to the operating OS and supporting software for the cluster. This was a major update to the previously installed RedHat version (RHEL 6.6) up to CentOS 7.1. This provides newer versions of commonly used software and libraries, and will help us deliver more user-facing features in the coming months.
  • Cluster management software updates and reconfiguration. This includes Torque 6, which has a new set of resource options. The new Torque version will give better language for defining tasks, more consistent runtimes, and a platform for new  features.
  • The Flux Hadoop environment upgrade to Cloudera 5.7, which now includes Hive-On-Spark (the Hadoop cluster will return to service later this week).
  • /scratch on Flux updates.
  • Transition of the software modules environment to a system called Lmod. For more information, see our Lmod transition page. The complete Lmod User Guide can be found here: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/user-guide.

An HPC 2016 Upgrade Frequently Asked Questions page is available documenting a variety of issues related to the upgrades. Please direct any questions to hpc-support@umich.edu.

New ARC Connect service provides desktop graphical interface for HPC resources

By | Educational, Flux, General Interest, News | No Comments

Users of ARC-TS computing resources can now use desktop versions of popular software packages like Matlab and R while accessing the Flux shared computing cluster. The new service, called ARC Connect, provides an easily accessible graphical user interface that simplifies doing interactive, graphical work backed by the high performance and large memory capabilities of the Flux cluster.

Using ARC Connect may benefit you if you need to:

  • Very easily interactively use graphical software on HPC clusters (Flux, Armis).
  • Do high performance, interactive visualizations.
  • Share and collaborate with colleagues on HPC-driven research.
  • Use HPC in teaching.
  • Access ARC HPC clusters from off-campus without using the U-M VPN.

Features:

  • Remote desktop sessions (VNC) for using Flux graphically and interactively.
  • Jupyter notebooks for Python and R (other languages coming soon).
  • RStudio interactive development environment for R.

Users can run desktop applications such as MATLAB or RStudio as if running on a laptop, but with all the power of Flux, as opposed to using them in batch mode or via text-only interactive sessions. Users can also use notebooks which require more processing power or memory than are available on their local computer or tablet (currently, Python and R notebooks are available).

ARC Connect is an enhanced version of the TACC / XSEDE Visualization Portal, and has been made possible at the University of Michigan through a collaboration between ARC Technical Services and the Texas Advanced Computing Center at the University of Texas.

For information on how to use ARC Connect, visit arc-ts.umich.edu/arc-connect. If you need further help, contact hpc-support@umich.edu.